Southeastern Rail customers are being advised to check before they travel, with normal services not expected to resume for the rest of this week.
Passengers have been battling cancellations, delays and diversions since a freight train derailed in Lewisham on Tuesday.
Train services will not be stopping at some stations.
There will be no Southeastern services at Charring Cross, Waterloo, Waterloo East, Cannon Street or London Bridge stations until August 29. Instead, trains will be diverted to Victoria, Blackfriars and New Cross.
Meanwhile buses will replace trains at Deptford, Greenwich, Maze Hill and Westcombe Park stations.
From August 29 to September 1, there will be no Southeastern services at Cannon Street, with trains instead diverted to Victoria, Blackfriars and New Cross.
Buses will replace trains at Deptford, Greenwich, Maze Hill and Westcombe Park stations.
The disruption is due to the continuing Thameslink programme work, which will see the new concourse at London Bridge open on August 29.
Disruption on Southeastern between London Bridge and Sevenoaks, and between Victoria and Sevenoaks due to person hit by a train at Orpington.
All lines are currently blocked. Trains may be diverted via Tonbridge.
Delays of up to 40 minutes on Southeastern between Ashford International and Victoria due to road vehicle hitting a bridge at West Malling.